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Octopuses can turn off Darwinism and edit their own genomes

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From Evolution News & Views:

Some stunning upsets in conventional thinking about evolution have hit the news in rapid succession, threatening Darwin’s famous tree icon.

Under the rules of neo-Darwinism, mutations must be random, providing fodder for the blind processes of natural selection. But here’s a case where animals defy their own neo-Darwinism. More.

Yes, octopuses edit their genomes:

News from the University of Chicago’s Marine Biological Laboratory implies that cephalopods were wise to choose the RNA editing bargain. “Mutation is usually thought of as the currency of natural selection, and these animals are suppressing that to maintain recoding flexibility at the RNA level,” says biologist Joshua Rosenthal. The lab “identified tens of thousands of evolutionarily conserved RNA recoding sites in this class of cephalopods, called coleoid.” Evolutionarily conserved is a euphemism for stability — for non-evolution — over long periods of time. Those squid are smart, all right: they seem to be able to prevent Darwinian evolution!

True, cephalopods are smart. But they didn’t think up the idea of stasis. And it may well turn out that dumb and dumber creatures can turn off Darwinian evolution too. It might be a survival feature.

Academic Darwinism would be in much more trouble if evidence mattered the way it used to.

See also: Furry, feathery, and finny animals speak their minds

Stasis: When life goes on but evolution does not happen

What the fossils told us in their own words

Follow UD News at Twitter!

Cephalopod intelligence is real but does not extend to gene editing:

14 Replies to “Octopuses can turn off Darwinism and edit their own genomes

  1. 1
    Bob O'H says:

    Denyse, no the work doesn’t show that octopodes can edit their genomes. Their DNA stays intact. No, octopi edit their RNA, which is not what’s inherited. The anonymous writer at EN&V doesn’t seem to get this either.

  2. 2
    Origenes says:

    Bob O’H: No, octopi edit their RNA, which is not what’s inherited. The anonymous writer at EN&V doesn’t seem to get this either.

    Bob, you are the one who didn’t get it.

    From the paper:

    We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites.

    [Noa Liscovitch-Brauer et al.]

    What part of “evolutionarily conserved” do you not understand?
    – – –
    More from the paper:

    The edited transcripts are translated into protein isoforms with modified functional properties. By comparing editing across coleoid taxa, we found that, unlike the case for mammals, many sites are highly conserved across the lineage and undergo positive selection, resulting in a sizable slow-down of coleoid genome evolution.

  3. 3
    Bob O'H says:

    Origenes – Nothing in what you quote says that octopi edit their DNA, does it? So how does it contradict what I wrote?

    The conservation is of DNA sequences around the sites that undergo RNA editing – basically there has to be a target for the enzyme to recognise, and this is what is conserved.

  4. 4
    Origenes says:

    Bob, your claim is that RNA-editing in octopi is not heritable.

    Bob O’H: No, octopi edit their RNA, which is not what’s inherited.

    You are mistaken. From the paper:

    Consistently, and in stark contrast with mammals, the higher the editing levels, the more sites are conserved (Figures 5C and 5D). Furthermore, editing is over-represented in highly conserved regions of the transcriptome (>95% identity between species) (Figure 5E). Taken together, these results suggest that recoding by RNA editing is commonly adaptive in coleoid cephalopods, with many thousands of recoding sites under positive selection.

  5. 5
    wd400 says:

    mRNA is not inherited and the genome is not edited in this case.

    The passages you quote are saying particular genes have their mRNAs edited consistently. That’s the result of plain old DNA inheritance.

    None of this has anything to do with “turning off Darwinism” either.

  6. 6
    Bob O'H says:

    Origenes – no, I don’t claim that RNA editing is not inherited. The machinery (including the targets of the enzymes) clearly is inherited. But the edited RNAs themselves are not inherited.

  7. 7
    Origenes says:

    wd400: The passages you quote are saying particular genes have their mRNAs edited consistently. That’s the result of plain old DNA inheritance.

    If the entire structure of those advantageous editing sites is indeed preserved in DNA, then it must span a large fraction of the genomic coding sequence. What does that tell us about the amount of junk-DNA in cephalopods I wonder?

    However, many other organisms, such as humans, edit abundantly, producing multiple promiscuous edits. What is unique about coleoid cephalopods is that they appear not to exclude editing from protein-coding regions, leading to many thousands of recoding sites being recruited and conserved across distant species.

    How unique are those cephalopods? There may indeed loom a more general threat to the junk-DNA narrative here:

    So far, news sources such as New Scientist are just calling this “a special kind of evolution” based on RNA editing instead of DNA mutations. They’re restricting the phenomenon to squid, octopuses and cuttlefish. But usually when a new process is discovered in one group, scientists — now alerted to it — start finding it in other groups, too.
    [ENV]

  8. 8
    wd400 says:

    If the entire structure of those advantageous editing sites is indeed preserved in DNA, then it must span a large fraction of the genomic coding sequence. What does that tell us about the amount of junk-DNA in cephalopods I wonder?

    Almost nothing. Parts of some introns will be conserved, as most RNA editing is focused on a duplexes formed at intron-exon boundaries. But that would account only for a tiny fraction of the total genome size, so I’m not sure what relevance that would have?

  9. 9
    Origenes says:

    wd400 @8

    So you are saying that preserving those RNA structures doesn’t require a large fraction of the genomic coding sequence? Only a tiny fraction of the total genome size?

  10. 10
    wd400 says:

    Yes.

  11. 11
    Origenes says:

    wd400 @8 @10

    I take it then that you do not agree with the paper:

    What is most surprising about cephalopod recoding is its effect on genome evolution. From a mechanistic standpoint, this makes sense. In order to edit a specific adenosine, ADAR requires surrounding RNA structures. Even single nucleotide substitutions within these structures can abolish editing (Reenan, 2005, Rieder et al., 2013). If an editing site is advantageous, the structure must be preserved. Abundant editing requires abundant structures that can span a large fraction of the genomic coding sequence. Thus, although extensive recoding presents the species with a route toward proteome complexity, it comes with its own price tag. The constraints required to preserve thousands of recoding sites reduce the accumulation of mutations at positions in the proximity of an editing site, slowing down the rate of conventional, DNA-level evolution.

  12. 12
    wd400 says:

    No. The paper says editing motifs may include a substantial proportion of the protein coding sequence. But, of, course the protein coding sequences are only a tiny portion of most animal genomes (molluscs included).

    A subset of that subset is indeed a tiny fraction of the genome.

  13. 13
    Origenes says:

    Abundant editing requires abundant structures that can span a large fraction of the genomic coding sequence.

    WD400: The paper says editing motifs may include a substantial proportion of the protein coding sequence.

    However, there is little reason to assume that preserving the information of editing motifs in DNA ia restricted to those sections of DNA that code for proteins. In fact, it makes more sense if it is not.
    IOWs it’s an open question how much of the cephalopod’s genome is involved in preserving this information.

  14. 14
    wd400 says:

    However, there is little reason to assume that preserving the information of editing motifs in DNA ia restricted to those sections of DNA that code for protein.

    I mean… how would you know? This is not a topic you have any knowledge in, why would you think you intuition added up to anything?

    In fact, research into RNA editing shows us that the motifs are on the order of a few tens of bp and act in cis. So they really are limited to protein coding genes (including intron boundaries).

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